data_3THW # _model_server_result.job_id xPpSbgZOo4qz11GI1p82GA _model_server_result.datetime_utc '2024-12-13 10:07:37' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3thw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":935}' # _entry.id 3THW # _exptl.entry_id 3THW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3THW _cell.length_a 105.84 _cell.length_b 116.13 _cell.length_c 180.04 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3THW _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order hydrog 'DC-DG PAIR' hydrog1 C N4 DC 1 D DC 1 1_555 C O6 DG 53 D DG 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N3 DC 2 D DC 2 1_555 C N1 DG 52 D DG 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N4 DC 2 D DC 2 1_555 C O6 DG 52 D DG 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C O2 DC 2 D DC 2 1_555 C N2 DG 52 D DG 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog5 C N3 DT 3 D DT 3 1_555 C N1 DA 51 D DA 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog6 C O2 DC 4 D DC 4 1_555 C N2 DG 50 D DG 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog7 C N3 DT 5 D DT 5 1_555 C N1 DA 49 D DA 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N1 DA 6 D DA 6 1_555 C N3 DT 48 D DT 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N6 DA 6 D DA 6 1_555 C O4 DT 48 D DT 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N3 DT 7 D DT 7 1_555 C N1 DA 47 D DA 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C O4 DT 7 D DT 7 1_555 C N6 DA 47 D DA 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N3 DC 8 D DC 8 1_555 C N1 DG 46 D DG 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N4 DC 8 D DC 8 1_555 C O6 DG 46 D DG 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C O2 DC 8 D DC 8 1_555 C N2 DG 46 D DG 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C N3 DT 9 D DT 9 1_555 C N1 DA 45 D DA 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C O4 DT 9 D DT 9 1_555 C N6 DA 45 D DA 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C N1 DG 10 D DG 10 1_555 C N3 DC 44 D DC 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N2 DG 10 D DG 10 1_555 C O2 DC 44 D DC 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C O6 DG 10 D DG 10 1_555 C N4 DC 44 D DC 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N1 DA 11 D DA 11 1_555 C N3 DT 43 D DT 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N6 DA 11 D DA 11 1_555 C O4 DT 43 D DT 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C N1 DA 12 D DA 12 1_555 C N3 DT 42 D DT 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N6 DA 12 D DA 12 1_555 C O4 DT 42 D DT 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N1 DG 13 D DG 13 1_555 C N3 DC 41 D DC 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C N2 DG 13 D DG 13 1_555 C O2 DC 41 D DC 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C O6 DG 13 D DG 13 1_555 C N4 DC 41 D DC 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog27 C O2 DC 14 D DC 14 1_555 C N1 DG 40 D DG 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C N3 DC 15 D DC 15 1_555 C N1 DG 35 D DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C N4 DC 15 D DC 15 1_555 C O6 DG 35 D DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C O2 DC 15 D DC 15 1_555 C N2 DG 35 D DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C N1 DG 16 D DG 16 1_555 C N3 DC 34 D DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C N2 DG 16 D DG 16 1_555 C O2 DC 34 D DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C O6 DG 16 D DG 16 1_555 C N4 DC 34 D DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N3 DT 18 D DT 18 1_555 C N1 DA 32 D DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C O4 DT 18 D DT 18 1_555 C N6 DA 32 D DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog36 C N4 DC 19 D DC 19 1_555 C O6 DG 31 D DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C N1 DG 20 D DG 20 1_555 C N3 DC 30 D DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C N2 DG 20 D DG 20 1_555 C O2 DC 30 D DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C O6 DG 20 D DG 20 1_555 C N4 DC 30 D DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N1 DA 21 D DA 21 1_555 C N3 DT 29 D DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C N6 DA 21 D DA 21 1_555 C O4 DT 29 D DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DC MISPAIR' hydrog42 C O4 DT 22 D DT 22 1_555 C N4 DC 27 D DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 C N3 DT 22 D DT 22 1_555 C N1 DA 28 D DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 C O4 DT 22 D DT 22 1_555 C N6 DA 28 D DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog45 C N1 DG 23 D DG 23 1_555 C O2 DC 27 D DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3THW _atom_sites.fract_transf_matrix[1][1] 0.009448 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008611 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005554 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 ADP A 1 935 1 ADP ADP . E 5 HOH A 1 936 1 HOH HOH . E 5 HOH A 2 937 2 HOH HOH . F 5 HOH B 1 3 3 HOH HOH . F 5 HOH B 2 4 4 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . D 4 0.319 7.024 -29.368 1 61.22 ? PB ADP 935 A 1 HETATM 2 O O1B ADP . . . D 4 -0.541 7.143 -28.136 1 60.72 ? O1B ADP 935 A 1 HETATM 3 O O2B ADP . . . D 4 1.777 6.761 -29.078 1 61.35 ? O2B ADP 935 A 1 HETATM 4 O O3B ADP . . . D 4 0.068 8.087 -30.411 1 56.53 ? O3B ADP 935 A 1 HETATM 5 P PA ADP . . . D 4 -1.747 5.378 -30.286 1 67.35 ? PA ADP 935 A 1 HETATM 6 O O1A ADP . . . D 4 -2.313 4.808 -29.006 1 68.07 ? O1A ADP 935 A 1 HETATM 7 O O2A ADP . . . D 4 -2.369 6.604 -30.905 1 65.89 ? O2A ADP 935 A 1 HETATM 8 O O3A ADP . . . D 4 -0.179 5.66 -30.066 1 65.94 ? O3A ADP 935 A 1 HETATM 9 O O5' ADP . . . D 4 -1.74 4.226 -31.409 1 73.91 ? O5' ADP 935 A 1 HETATM 10 C C5' ADP . . . D 4 -2.946 3.88 -32.086 1 80.23 ? C5' ADP 935 A 1 HETATM 11 C C4' ADP . . . D 4 -2.685 2.691 -33.001 1 86.71 ? C4' ADP 935 A 1 HETATM 12 O O4' ADP . . . D 4 -1.858 1.743 -32.329 1 88.2 ? O4' ADP 935 A 1 HETATM 13 C C3' ADP . . . D 4 -3.974 1.985 -33.388 1 91.35 ? C3' ADP 935 A 1 HETATM 14 O O3' ADP . . . D 4 -4.207 2.129 -34.791 1 94.32 ? O3' ADP 935 A 1 HETATM 15 C C2' ADP . . . D 4 -3.767 0.524 -33.051 1 95.79 ? C2' ADP 935 A 1 HETATM 16 O O2' ADP . . . D 4 -3.874 -0.262 -34.239 1 100.45 ? O2' ADP 935 A 1 HETATM 17 C C1' ADP . . . D 4 -2.358 0.417 -32.492 1 94.4 ? C1' ADP 935 A 1 HETATM 18 N N9 ADP . . . D 4 -2.395 -0.242 -31.166 1 95.89 ? N9 ADP 935 A 1 HETATM 19 C C8 ADP . . . D 4 -2.508 0.395 -29.987 1 94.48 ? C8 ADP 935 A 1 HETATM 20 N N7 ADP . . . D 4 -2.51 -0.482 -28.952 1 96.82 ? N7 ADP 935 A 1 HETATM 21 C C5 ADP . . . D 4 -2.395 -1.715 -29.476 1 99.98 ? C5 ADP 935 A 1 HETATM 22 C C6 ADP . . . D 4 -2.333 -3.093 -28.94 1 103.71 ? C6 ADP 935 A 1 HETATM 23 N N6 ADP . . . D 4 -2.397 -3.325 -27.607 1 103.79 ? N6 ADP 935 A 1 HETATM 24 N N1 ADP . . . D 4 -2.211 -4.105 -29.827 1 107.01 ? N1 ADP 935 A 1 HETATM 25 C C2 ADP . . . D 4 -2.147 -3.881 -31.152 1 106.94 ? C2 ADP 935 A 1 HETATM 26 N N3 ADP . . . D 4 -2.196 -2.658 -31.708 1 103.65 ? N3 ADP 935 A 1 HETATM 27 C C4 ADP . . . D 4 -2.318 -1.553 -30.936 1 100.24 ? C4 ADP 935 A 1 # _model_server_stats.io_time_ms 119 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #